Sunday, January 29, 2012

For the first few years of school, I got by with what I thought I could best afford: Pop-tarts, cereal, trail mix, yogurt, or corn meal mush. I realized (much later) that these foods, cheap though they were, wouldn't sustain me for the long morning push of reaction set-ups, group meetings, and seminars. It's also not a great idea to supplant the need for proper nutrition with more coffee - not if you want to sleep at night! (Do chemists sleep, anyway?)

Thus began my long experiment to find alternative (cheap!) breakfast ideas. Early on, I realized that the little café a few blocks from campus had it right: they microwaved egg mixture, slapped some cheese on it, and popped it onto a bagel...and charged you $4.50! I thus embarked on a quest to learn how to construct a bagel sandwich for myself, using only what was in our lab break room: a fridge, plastic forks and spoons, a microwave, and a toaster.

Procedure - Spray inner surface of small plastic dish with cooking spray. Mix egg and milk together with plastic fork in dish, add spices to taste. Fold paper towel in half lengthwise, and cover dish by "wrapping" towel over the top and tucking ends under the bottom (in case egg explodes from excess heat).

Place bagel in toaster and commence toasting. In the meantime, set microwave (assumes a 120V, 2 Amp microwave) for a single cycle of 48 seconds at 60%Power. Remove dish, lightly "shake" to ensure cooking is even, re-cover with towel, and place in for a second cycle of 50 seconds at 90% Power. Now add your cheese, and microwave one last time (uncovered, this time) for 10 seconds at full power. This should melt the cheese.

Did your bagel finish toasting? Great! Take one half of the bagel, and place it over the plastic dish. Invert the entire thing (a "puck" of cooked egg should slide out), and top with final bagel slice. If this still isn't enough food, consider adding some spinach leaves, apple slices, or microwaved bacon / ham to augment.

Saturday, January 28, 2012

NPR reports that the US FDA recently detained several shipments of orange juice imported from Brazil. The agency received a December 2011 tip-off from a juice company (Minute Maid, via parent company Coca-Cola) that the imports contained low concentrations of the fungicide carbendazim. While this amount is unlikely to harm anyone, FDA indicated in its letter that the EPA hasn’t established safe levels for the compound in juice, and thus considers it an unlawful additive.

Carbendazim, a benzimidazole (a two-ringed aromatic structure with two nitrogens) metabolite of benomyl, was first prepared as a discrete compound by DuPont in the early 1960’s. It’s approved in several other countries to treat black spot, Dutch elm disease, powdery mildew, and a host of other fungal diseases. The fantastic NIH resource Toxnet tells us that carbendazim is a “Group C Possible Human Carcinogen,” but given how many different standards exist for this metric, what does that mean?

Diving deeper into the data, carbendazim appears to be both a teratogen (meaning it impairs fertility or embryonic development), and causes chromosomal aberrations; both effects appear at relatively high doses that you wouldn’t drink in a single glass of OJ.

The unspoken fear here may be long-term exposure. Consider other recent reports on the ability of PFC’s (perfluorinated compounds, like the long-chain PFOS found in Scotchgard) to decrease vaccine response. Or, read the never-ending list of maladies brought on by exposure to phthalates, omnipresent plasticizers known to cause endocrine disruption. Health risks from accumulated compound may prompt the FDA’s proactive stance towards even tiny amounts of this fungicide in imported juice.

Surly Chemist Soapbox Moment – Both NPR reports refer to their subjects as “chemicals” sometimes as early on as the article’s title! The connotation for this word is overwhelmingly negative, which should be apparent from the “chemical-free” movement and the interchangeable use of “chemical” with toxin, poison, or contaminant. Doesn’t chemistry already have image problems?

Here are a few chemical synonyms for the next go-around: compound, moiety, substance, entity, additive, species, or molecule. None of these are perfect for every situation, but any would be preferable over the catch-all, “chemical.”

Tuesday, January 24, 2012

Did folks tune in to watch President Barack Obama present the 2012 State of the Union tonight?

Out of sheer curiosity, I downloaded the text to both the 2011 SoTU (Winning the Future) and the 2012 speech (An America Built to Last). Now, I’m no political pundit or news analyst - I’m a scientist. So, I thought an interesting game might be to see how certain scientific themes grew or shrunk over the past 365 ¼ days.

Is there a take-home message to counting up words and relating them to the direction of the country? Perhaps not. Thematically, the two speeches were different: 2011 was more forward-looking and focused on education, business, and terrorism; while 2012 dealt with global politics, congressional reform, and taxes.

But there exists notable declines in most science-related topics from last year’s speech to this one. Except, of course, on topics where economics and science often cross – substantial mentions of oil and energy.

Saturday, January 21, 2012

I’ll admit it: I love to look at antiquated predictions of how the world will be in 50 or 100 years. These glimpses into the future strongly reflect their era; the audience had to grasp the author’s intent and direction using metaphors and extensions of the technology they knew.

We chuckle at predictions such as world zeppelin travel and automated horse-carriages, much like future generations might wrinkle their noses at our notion of a “world wide web” or “smart phones.”

A new (old!) article, published in the 1901 Ladies’ Home Journal by one John Elfreth Watkins, Jr., puts forth several such predictions (thanks to the Saturday Evening Post and the BBC; see reddit or imgur for the full article). Mr. Watkins apparently spoke with “the wisest and most careful men in our greatest institutions of science and learning” in a quest to determine what “…will have been wrought…before the dawn of 2001.”

All told, Mr. Watkins made 28 predictions in his article, and the BBC article covered 14, the Post 17. Since this is primarily a science blog, I’ll comment on some of the tech highlights; sadly, most of these didn’t make the cut for the preceding articles.

The drug designer's "killer app"

“Few drugs will be swallowed or taken into the stomach” – Drug designers, aiming always for the killer app of oral availability, would be amused to hear this. The author was correct about a later statement in this section, though: “The living body will to all medical purposes be transparent.” Mr. Watkins waxes about invisible rays allowing physicians to operate on human organs directly, which, with the advent of MRI, PET scans, and endoscopy, is much closer to reality.

“There will be no C, X, or Q in our every-day alphabet” – Uh-oh, don’t tell any organic chemists! C is, of course, carbon, and X is a placeholder for halogens, a math variable, part of road signs (X-ing), holidays (Xmas), and of course where pirates bury their treasure!

“The soil will be kept enriched by plants which take their nutrition from the air and give fertility to the earth” – Nitrogen fixation, anyone? Legumes such as peas, beans, and carob are often rotated in with other food crops to ensure proper soil nutrients. In 1901, Watkins still had no inkling of the Great War to come, or how the Haber-Bosch process would lead to cheap fertilizers and increased munitions.

“Plants will be made proof against disease microbes just as readily as man is to-day against smallpox” – Mr. Watkins refers, of course, to Jenner’s development of the cowpox vaccine for smallpox treatment. In the 21st Century, industrial conglomerates such as Dow Agro, DuPont Crop Science, BASF, Syngenta, and Monsanto work towards pest-resistant crops and pesticides.

An FDA inspector checks a salad bar. Source: FDA Flickr.(Did you know the FDA maintains a Flickr account? I didn't!)

“Storekeepers who expose food to air breathed out by patrons or to the atmosphere of the busy streets will be arrested with those who sell stale or adulterated produce” – The modern FDA, presaged 5 years before its formation in 1906, now inspects both food and drugs from production through sale to consumers.

Since I started this blog last year, I’ve looked back often at the tongue-in-cheek title. I thought that, like Derek’s delectableexperiments, perhaps I should chime in with an offering of my own. However, I thought I’d aim for the opposite end of the culinary spectrum: the starving grad student.

"Piled Higher and Deeper" by Jorge Cham - www.phdcomics.com

Back in school, I not so fondly remember weekends where I had about $5 in my pocket until my next stipend check came in. Sometimes, a trip to McDonald's seemed like a fancy night out. Most of the time, though, I fell back on some tried-and-true favorites: soup, frozen broccoli, ramen noodles, or oatmeal.

But in terms of cost : hunger ratio, I never found a better recipe than this, a See Arr Oh family classic:

Procedure – Bring 3 cups of water to a rapid boil. In a separate bowl, pre-mix the cold water, salt, and corn meal together until a loose suspension (no clumps!) forms. Quickly pour the mixture into the boiling water with stirring, and reduce the burner heat to medium-low. Cover pot. Simmer the thickening corn mixture for about 7 minutes, stirring occasionally.

We serve this warm at breakfast, with butter, pepper, and white sugar. I could imagine it seasoned to taste for dinner (cumin, hot sauce, red pepper, soy), or perhaps as a side dish (paprika, parsley, thyme) to a meat or vegetable.

Total Cost: $0.30-0.50 per serving, depending on spices and seasonings

Thursday, January 5, 2012

The other night, my special someone and I were sitting on the couch, and I was introduced to the "new hot thing" in fashion: magnetic nail polish.

Apparently, as several DIYblogs explain, the "secret magnetic particles" contained in the polish "activate" in a magnetic field. Of course, a quick glance at the ingredients shows just plain iron powder, which, when dolled up with several layers of lacquer and clays, creates ripple patterns on the nail surface.

But hey, with companies like LCN and Sephora charging to the tune of $16 USD (for a 10 mL bottle!) the price is comparable to standard labreagents.

Sodium Zeolite A
Source: British Zeolite Association

But I digress. Looking through the ingredient list of the Trafalgar Square color, I felt totally out of my depth. Luckily, C&EN's "What's That Stuff?" feature came to my rescue, at least for a few of the common components (thanks, Carmen!).

Of course, there's nitrocellulose, the shiny, potentially explosive major player, found for a time in movie film, gun cotton, and auto paint. Clays familiar to the bench chemist (bentonites, hectorites) make their way in as thickeners, including the fantastically-named bulking agent fluorophlogopite. This synthetic aluminosilicate calls to mind zeolites, inorganic structures used in fuel upgrading, gas storage, and catalysis.

One of the great features of chemical research: Even though you think you've seen it all, there's a surprise around the corner. After nitrocellulose, this particular brand uses an interesting copolymer of adipic acid, neopentyl glycol, and...trimellitic anhydride? I'd seen the first two, but never this, an interesting "triple-reactive" crosslinker (looks like maleic anhydride went for a crazy aromatic spin) which was first isolated in 1830 by Liebig and Wöhler, two heavyweights of 19th Century German chemistry.

This tetracyclic curing agent, an all-star of the coal tar chemistry in the early 1900s, found use as a curing agent in polymers as early as the '30s. New uses in the last 15 years include protein charge ladders and luminescent materials research.

Update (1/21/2012): Over at Chemical Novelty, Travis has dug deep in the patent literature to really see what this product is all about. Go have a peek!

While browsing on Nature News this afternoon, I came across a puzzling chemical graphic in the article "Frontier Experiments: Tough Science." Under the heading "Seeing through the molecular mirror," came this picture of two hands, showing the chirality around a Re center...

Source: Thomas Porostocky / Nature News

OK, I understand the point of the graphic, but I'd like to tackle a few pedagogical questions. First, has anyone ever seen a real-life compound like this? I searched Reaxys, but couldn't find any examples of a Re center bound to three different chalcogens. Closest I could find were some rhenium selenide clusters.

Second, what's the valency around that Re center? My good buddy Wikipedia (source of all truthful information on the internet, right?) informs me that Re can have oxidation numbers from -1 to +7. Well, OK, so I'll assume double bonds between all the heteroatoms and Re (which also doesn't come up via Reaxys or our buddy Google), but I'd still question whether, as drawn, we have Re(+4), five, six, or seven!

So let's assume a stable compound...is it actually "chiral?"

Textbooks on inorganic chemistry indicate that Re(VII) complexes with oxo ligands prefer the square pyramidal geometry. Well, you say, it has two other bivalent chalcogens, so maybe it's tetrahedral after all? My ligand field theory spider sense tells me that Re(VII) is d0, which should have a tetrahedral geometry, but I don't know enough about this peculiar complex to know if it takes on solvent molecules (becoming octahedral?) or undergoes inversion. Maybe in the gas phase (lasers!), in a vacuum, it's just a plain ol' tetrahedron.

I'm not attacking the artist, he's a graphical designer, not a chemist. And I get the message - it's a physical chemistry model experiment to show how chiral molecules show slightly different physical parameters, perhaps ones that can be measured. The designers use a single periodic column to show how molecular number assigns chirality (C-I-P convention) and to enforce a striking enantiomeric disparity. It's just hard for me, as a non-physical chemist, to go this far out on the edge.

Please, to illustrate this concept, let's use known examples (amino acids, anyone?) first, and then transition out to the edge. Then we won't suffer Feynman's cargo cult caveat: "...you should not fool the layman when you're talking as a scientist."

Update (1/5/12, 3:44PM) - I realize that the Darquie experiments referred to in the text involve (potential) formation of such a compound. I simply find "strange bedfellows" for text that leads with biological homochirality, since Re(VII) compounds are unlikely to be something one encounters in cells!

Tuesday, January 3, 2012

I'd like to highlight a specific article, titled "From the Analyst's Couch - A Decade of Drug Discovery." Written by one John Arrowsmith (of Thomson-Reuters data-crunching fame), it shows how the major players in the pharma biz have juggled around in the past 10 years. Note Roche and Novartis' upward trend: from 2001-2011, Roche went from 10th to 5th in market cap, and Novartis from 5th to 3rd.

Source: Thomson Reuters

Not bad at all. Any specific reasons behind those climbs? First, Roche's acquisition of Genentech certainly helped them out, with less of the messy transitions of the Pfizer-Wyeth or Merck-Schering mergers. Second, look at the massiveuptick in R&D spending by Roche (blue) and Novartis (pink) over the past decade!

Unless I'm mistaken, I read both companies' spending as roughly quadrupling, from ~$2 billion to nearly $8-9ish billion over the past decade. Wow.

Note also that Pfizer, making double their Lipitor take from a decade past, still showed mostly flat investment in R&D from 2003-2009.

Page Two shows us a bar graph of the radical shift in therapeutic areas (this include all drugs from P1 -> NDA).

Source: Thomson Reuters

Looks like cancer meds / pain / diabetes are WAY up, and cardiovascular is way down.

See Arr Oh

Who is this masked chemist?

Finding my way through new challenges.
I was a founding blogger at Scientific American's Food Matters and Blog Syn. I once wrote for C&EN's The Haystack. I've written for Nature Chemistry, Newscripts, Chemistry Blog, Chemjobber, and Totally Synthetic.